Question: Gene annotation pipeline for bacteria
gravatar for bird77
4.0 years ago by
bird7770 wrote:

I have a draft genome of a alpha-proteobacterium (genome size about 8Mbp) and I want to perform gene prediction and annotation.

Until now, I have used the RAST server for this task, but the amount of predicted genes with the annotation "hypothetical protein" is very high (about 60%).

What can you recommend for prokaryotic gene prediction and annotation workflows (I certainly can also combine different tools for gene prediction and annotation, but I do not know what the current standard is)?

Thank you so much for your assistance.

annotation genome • 1.7k views
ADD COMMENTlink modified 3.0 years ago by predeus1.4k • written 4.0 years ago by bird7770
gravatar for colindaven
4.0 years ago by
Hannover Medical School
colindaven2.6k wrote:

Have a look at Prokka by Torsten Seeman, or the recent Genix.

Other places also have web based annotation pipelines, the NCBI one probably still exists.

ADD COMMENTlink written 4.0 years ago by colindaven2.6k
gravatar for predeus
3.0 years ago by
predeus1.4k wrote:

Prokka is probably most used in the field now. Using --proteins with a specific database (e.g. species-specific) seems like a good way to annotate most of the ORFs. Just make sure you get the reference proteins in the right format - they need to look something like this:

>gene_id ~~~gene_name~~~putative protein function

There are few scripts to make your protein annotations look like this. the problem is discussed in one of the issues on Prokka github repository.

ADD COMMENTlink written 3.0 years ago by predeus1.4k
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